bacteria_processing_1.md

bacteria_processing_1

Ilya 1/28/2019

install and load required packages

## Removing package from '/Library/Frameworks/R.framework/Versions/3.4/Resources/library'
## (as 'lib' is unspecified)
## Removing package from '/Library/Frameworks/R.framework/Versions/3.4/Resources/library'
## (as 'lib' is unspecified)

## 
## Attaching package: 'rlang'

## The following object is masked from 'package:data.table':
## 
##     :=

## 
## The downloaded binary packages are in
##  /var/folders/0d/qm_pqljx11s_ddc42g1_yscr0000gn/T//RtmpCE1SUw/downloaded_packages
## 
## The downloaded binary packages are in
##  /var/folders/0d/qm_pqljx11s_ddc42g1_yscr0000gn/T//RtmpCE1SUw/downloaded_packages

## 
## Attaching package: 'dplyr'

## The following object is masked from 'package:glue':
## 
##     collapse

## The following objects are masked from 'package:data.table':
## 
##     between, first, last

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

## 
## Attaching package: 'reshape2'

## The following objects are masked from 'package:data.table':
## 
##     dcast, melt

## corrplot 0.84 loaded

## Loading required package: lattice

## Loading required package: survival

## Loading required package: Formula

## Loading required package: ggplot2

## 
## Attaching package: 'Hmisc'

## The following objects are masked from 'package:dplyr':
## 
##     src, summarize

## The following objects are masked from 'package:base':
## 
##     format.pval, units

## CHNOSZ version 1.1.3 (2017-11-13)

## Please run data(thermo) to create the "thermo" object

## 
## Attaching package: 'CHNOSZ'

## The following objects are masked from 'package:Hmisc':
## 
##     mtitle, spearman

## The following object is masked from 'package:dplyr':
## 
##     slice

## Skipping install of 'taxizedb' from a github remote, the SHA1 (7ee9741a) has not changed since last install.
##   Use `force = TRUE` to force installation

## 
## Attaching package: 'taxizedb'

## The following objects are masked from 'package:taxize':
## 
##     children, classification, downstream

1. Get bacteria-caused dx in GIDEON

2. Match dx to pathogen spp. names

3. Match spp. names (from GIDEON zdx and GMPD) to traits (in GMPD & other)

4. Compile master list of bacteria spp & traits

5. Feature construction with bacterial traits

6. Data visualization: summary “state of knowledge” on bacteria causing disease in mammals or humans

7. Use traits to predict transmissibility and human disease outcomes

2. Match dx to pathogen spp. names

Include non-zoonotic pathogenic bacteria

get zoonotic and non-zoonotic pathogens from GMPD and assign taxonomic ID only for those that are species-level

select only bacteria using info in G_taxonomy

source("R_name2taxid_GMPD.R")

## [1] TRUE
## [1] 2362

# source(paste0(wd,"/R_name2taxid_GMPD.R"))
# ../CODE/DATA_PROCESSING/

classify pathogens in GMPD to order, family, genus. Make G_classified.Rdata and save

source("R_classify_bacteria_observed_GMPD.R")

##       user     system    elapsed 
## 0.69635000 0.02011667 0.71906667

load data on zoonotic bacteria

# source("R_human_zoonotic_non_zoonotic1.R")